def strip(root, amber_prmtop, messages):
""" Strips a mask from the topology file """
if amber_prmtop.parm.chamber:
showerror('Not Implemented', 'The strip command does not yet work with ' +
'chamber topologies')
return
# We need a mask, new radius, new epsilon, and for chamber topologies,
# a new radius-1-4 and epsilon-1-4. Don't add the latter ones until we
# know if we have a chamber prmtop or not.
widget_list = [('MaskEntry', 'Atoms to strip from topology')]
# We need 5 string variables, then get the description.
var_list = [StringVar()]
description=('Strips the selected atoms from the topology file. All\n' +
'remaining atoms and parameters remain unchanged. Any\n' +
'parameters associated with stripped atoms are removed.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('addLJType', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
var = var_list[0]
if not var.get(): return
try:
action = ParmedActions.strip(amber_prmtop, ArgumentList(var.get()))
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def printinfo(root, amber_prmtop, messages):
""" Prints all of the info in a given FLAG """
# Set up the window
# variables we need for printInfo
widget_list = [('Entry', '%FLAG you want info from')]
# Variable list -- we need a single string
var_list = [StringVar()]
# description
description = ' '.join(ParmedActions.printinfo.__doc__.split())
cmd_window = _guiwidgets.ActionWindow('printInfo', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Make sure we didn't cancel (or just press OK with no input), or just leave
var = var_list[0].get()
if not var: return
# Now that we did something, do it
action = ParmedActions.printinfo(amber_prmtop, ArgumentList(var))
if not action.found:
showerror('Not Found!', '%%FLAG %s not found!' % var.upper())
return
window = Toplevel(root)
window.resizable(True, True)
window.title('%%FLAG %s Info in %s' % (var.upper(), amber_prmtop))
text = _guiwidgets.ExitingScrollText(window, None, spacing3=5, padx=5,
pady=5, width=82, height=20)
text.write(action)
text.pack(fill=BOTH, expand=1)
window.wait_window()
messages.write('Wrote info for flag %s\n' % var.upper())
def change(root, amber_prmtop, messages):
""" Allows us to change a specific atomic property """
# The spinbox is sent with the Spinbox, label, and then a list of all of the
# values to give to it
widget_list = [('Spinbox', 'Property to change', 'CHARGE', 'MASS',
'RADII', 'SCREEN', 'ATOM_NAME', 'AMBER_ATOM_TYPE',
'ATOM_TYPE_INDEX', 'ATOMIC_NUMBER'),
('MaskEntry', 'Atoms to change'),
('Entry', 'New Value for Property')]
# We need 3 string variables, then get the description
var_list = [StringVar(), StringVar(), StringVar()]
description = 'Changes the property of given atoms to a new value'
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('change', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, store them and pass it to the class
var_list = [v.get() for v in var_list]
try:
action = ParmedActions.change(amber_prmtop, ArgumentList(var_list))
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def writeoff(root, amber_prmtop, messages):
""" Dumps an OFF library to a given filename """
fname = save_file_chooser('OFF library', '.lib')
if fname:
action = ParmedActions.writeoff(amber_prmtop, ArgumentList(fname))
messages.write('%s\n' % action)
action.execute()
def writefrcmod(root, amber_prmtop, messages):
""" Dumps an frcmod file to a given filename """
fname = save_file_chooser('frcmod', '.frcmod')
if fname:
action = ParmedActions.writefrcmod(amber_prmtop, fname)
action.execute()
messages.write('%s\n' % action)
def changelj14pair(root, amber_prmtop, messages):
""" Changes specific 1-4 Lennard Jones pairs """
# Only good for chamber topologies
if not amber_prmtop.parm.chamber:
showerror('Incompatible',
'changeLJ14Pair is only valid for chamber topologies!')
return
# variables we need for changelj14pair
widget_list = [('MaskEntry', 'Atom(s) Type 1 Mask'),
('MaskEntry', 'Atom(s) Type 2 Mask'),
('Entry', 'Combined Radius'),
('Entry', 'Combined Well Depth')]
# Variable list -- we need 2 masks and 2 floats
var_list = [StringVar(), StringVar(), StringVar(), StringVar()]
# description
description = ' '.join(ParmedActions.changeljpair.__doc__.split())
cmd_window = _guiwidgets.ActionWindow('changeLJ14Pair', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Make sure we didn't cancel (or just press OK with no input), or just leave
vars_exist = True in [bool(v.get()) for v in var_list]
if not vars_exist: return
# Now that we did something, do it
var_list = [v.get() for v in var_list]
try:
action=ParmedActions.changelj14pair(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
def changeljsingletype(root, amber_prmtop, messages):
""" Changes radius/well depth of a single LJ type given by the mask """
# We need a mask, radius, and well depth
widget_list = [('MaskEntry', 'Mask to change LJ Type'),
('Entry', 'New LJ Radius'), ('Entry', 'New LJ Depth')]
var_list = [StringVar(), StringVar(), StringVar()]
description = "Change a given atom type's LJ radius and well depth"
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('changeLJSingleType', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# addljtype expects any _non_specified variables to be None
var_list = [v.get() for v in var_list]
for i, v in enumerate(var_list):
if not v: var_list[i] = None
# If we did, store them and pass it to the class
try:
action = ParmedActions.changeljsingletype(amber_prmtop,
ArgumentList(var_list))
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def addexclusions(root, amber_prmtop, messages):
""" Adds atoms to other atoms' exclusion list """
# We need 2 masks
widget_list = [('MaskEntry', 'Atoms to add excluded atoms to'),
('MaskEntry', 'Atoms to exclude from other mask')]
# We have 2 mask variables
var_list = [StringVar(), StringVar()]
# Description
description=('Allows you to add arbitrary excluded atoms to exclusion\n' +
'lists. This omits all non-bonded interactions in the direct-space\n' +
'calculation, but does not omit interactions from adjacent cells in\n' +
'periodic simulations')
cmd_window = _guiwidgets.ActionWindow('addExclusions', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Bail out if we didn't get any variables
if not True in [bool(v.get()) for v in var_list]: return
var_list = [v.get() for v in var_list]
try:
action = ParmedActions.addexclusions(amber_prmtop, ArgumentList(var_list))
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def setangle(root, amber_prmtop, messages):
""" Sets (adds or changes) an angle in the topology file """
# We need 3 masks, a force constant, and an equilibrium angle
widget_list = [('MaskEntry', 'First atom in angle'),
('MaskEntry', 'Second (middle) atom in angle'),
('MaskEntry', 'Third atom in angle'),
('Entry', 'Force constant (kcal/mol rad**2)'),
('Entry', 'Equilibrium Angle (Degrees)')]
# We need 5 variables
var_list = [StringVar(), StringVar(), StringVar(), StringVar(), StringVar()]
description = ('Sets an angle in the topology file with the given Force ' +
'constant in kcal/mol/rad**2\nand the given equilibrium ' +
'angle in Degrees. All three masks must specify only a\n' +
'single atom. If the angle exists, it will be replaced. If ' +
'it doesn\'t, it will be added.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('setAngle', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, pass them through
var_list = [v.get() for v in var_list]
try:
action = ParmedActions.setangle(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def addpdb(root, amber_prmtop, messages):
""" Adds PDB information to a topology file """
# Get the name of the file
type_list = [('PDB', '*.pdb'), ('All Files', '*')]
fname = file_chooser('PDB File', type_list)
if not fname: return
widget_list = [('Checkbutton', 'Require all residue names be consistent.'),
('Checkbutton', 'Print element names in %FLAG ELEMENT'),
('Checkbutton', 'Print all insertion codes, even if all are '
'blank.')]
var_list = [StringVar(value='no') for i in range(3)]
description = ('Adds information from the PDB file (e.g., CHAIN IDs) to '
'the topology file')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('addPDB', amber_prmtop, widget_list,
var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
newvars = [fname]
# If we did, pass them through
if var_list[0] == 'yes': newvars.append('strict')
if var_list[1] == 'yes': newvars.append('elem')
if var_list[1] == 'yes': newvars.append('allicodes')
try:
action = ParmedActions.addpdb(amber_prmtop, ArgumentList(newvars))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def deletedihedral(root, amber_prmtop, messages):
""" Deletes a dihedral between 4 given atoms """
# We need 4 masks
widget_list = [('MaskEntry', 'First (end) atom in dihedral'),
('MaskEntry', 'Second (middle) atom in dihedral'),
('MaskEntry', 'Third (middle) atom in dihedral'),
('MaskEntry', 'Fourth (end) atom in dihedral')]
# We need 4 variables
var_list = [StringVar() for i in range(4)]
description = ('Deletes dihedrals between the atoms specified in mask1, ' +
'mask2, mask3, and mask4.\nIt will try to match dihedrals ' +
'only in the order given or reverse order. Dihedrals are\n' +
'specified by atom N in mask1, mask2, mask3, and mask4,' +
'where N is the selected\natom in that mask.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('deleteDihedral', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, pass them through
var_list = [v.get() for v in var_list]
try:
action = ParmedActions.deletedihedral(amber_prmtop,ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def hmassrepartition(root, amber_prmtop, messages):
"""
Repartitions mass by making H-atoms heavier and attached heteroatoms
lighter by the same amount to preserve the same total mass
"""
# The spinbox is sent with the Spinbox, label, and then a list of all of the
# values to give to it
widget_list = [('Entry', 'New hydrogen mass (daltons)'),
('Checkbutton', 'Repartition waters?')]
# We need 2 string variables, then get the description
var_list = [StringVar(value='3.024'), StringVar(value='no')]
description = ('Repartitions atomic masses to keep total mass the same '
'while increasing H-atom masses to allow using a larger '
'time step.')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('HMassChange', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = var_list[0].get() or var_list[1].get()
if not vars_found: return
# If we did, store them and pass it to the class
var_list = [v.get() for v in var_list]
# Convert the check button into the correct keyword
if var_list[1] == 'yes':
var_list[1] = 'dowater'
else:
var_list[1] = ''
try:
action = ParmedActions.hmassrepartition(amber_prmtop,
ArgumentList(var_list))
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def scale(root, amber_prmtop, messages):
""" Allows us to scale every value in a particular prmtop section """
# The spinbox is sent with the Spinbox, label, and then a list of all of the
# values to give to it
changeable_properties = ['Spinbox', 'Property to scale']
for flag in amber_prmtop.parm.flag_list:
if amber_prmtop.parm.formats[flag].type is float:
changeable_properties.append(flag)
widget_list = [changeable_properties, ('Entry', 'Value to scale by')]
# We need 2 string variables, then get the description
var_list = [StringVar(), StringVar()]
description = 'Scales all values in a given prmtop section by a given value'
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('scale', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = var_list[0].get() or var_list[1].get()
if not vars_found: return
# If we did, store them and pass it to the class
var_list = [v.get() for v in var_list]
try:
action = ParmedActions.scale(amber_prmtop, ArgumentList(var_list))
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def printdetails(root, amber_prmtop, messages):
""" Prints details about a given Amber mask """
title = 'Print Details'
mask = StringVar()
cmd_window = Toplevel(root)
cmd_window.title(title)
mask_entry = _guiwidgets.MaskEntry(cmd_window, amber_prmtop,
'Input an Amber Mask', mask, cmd_window)
mask_entry.config(pady=10)
mask_entry.grid(row=0, column=0, sticky=N+E+S+W)
button = Button(cmd_window, text='OK / Quit', command=cmd_window.destroy)
button.grid(row=1, column=0, sticky=N+E+S+W)
cmd_window.wait_window()
if not mask.get(): return
# Print our mask
window = Toplevel(root)
window.resizable(True, True)
window.title('Atom information for mask %s' % mask.get())
text = _guiwidgets.ExitingScrollText(window, None, spacing3=5, padx=5,
pady=5, width=100, height=20)
text.pack(fill=BOTH, expand=1)
action = ParmedActions.printdetails(amber_prmtop, mask.get())
text.write(action)
messages.write('Printed Amber Mask details on [%s]\n' % mask.get())
window.wait_window()
def changeljpair(root, amber_prmtop, messages):
""" Changes a pair-wise LJ interaction for pre-combined epsilon/Rmin """
# The variables we need for changeljpair
widget_list = [('MaskEntry', 'Atom(s) Type 1 Mask'),
('MaskEntry', 'Atom(s) Type 2 Mask'),
('Entry', 'Combined Radius'),
('Entry', 'Combined Well Depth')]
# Variable list -- we need 2 masks and 2 floats
var_list = [StringVar(), StringVar(), StringVar(), StringVar()]
# description
description = ' '.join(ParmedActions.changeljpair.__doc__.split())
cmd_window = _guiwidgets.ActionWindow('changeLJPair', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Make sure we didn't cancel (or just press OK with no input), or just leave
vars_exist = True in [bool(v.get()) for v in var_list]
if not vars_exist: return
# Now that we did something, do it
var_list = [v.get() for v in var_list]
try:
action = ParmedActions.changeljpair(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
def lmod(root, amber_prmtop, messages):
""" Prepares a prmtop file for use with lmod """
response = askyesno('lmod', 'Do you want to adjust LJ A-coefficients for '
'use with lmod?')
if response:
action = ParmedActions.lmod(amber_prmtop, ArgumentList(''))
action.execute()
messages.write('%s\n' % action)
def do_parmout(self, line):
# Store this action for later use. This action is unique
try:
self.parmout = ParmedActions.parmout(self.parm, line)
except ParmError, err:
self.stdout.write('Action parmout failed.\n\t')
self.stdout.write('%s: %s\n' % (type(err).__name__, err))
if self._exit_on_fatal:
raise err
def outparm(root, amber_prmtop, messages):
""" Output a final topology file """
fname = [save_file_chooser('prmtop', '.prmtop')]
if hasattr(amber_prmtop, 'rst7') and fname:
fname.append(save_file_chooser('inpcrd', '.inpcrd'))
if fname:
action = ParmedActions.outparm(amber_prmtop, ArgumentList(fname))
messages.write('%s\n' % action)
action.execute()
def deletepdb(root, amber_prmtop, messages):
""" Asks the user if they want to delete the sections added by addPDB """
response = askyesno('deletePDB',
'Do you want to delete the addPDB flags from %s?' %
amber_prmtop.parm)
if response:
action = ParmedActions.deletepdb(amber_prmtop, ArgumentList(''))
action.execute()
messages.write('%s\n' % action)
def do_source(self, line):
action = ParmedActions.source(self.parm, line)
self.stdout.write('%s\n' % action)
_cmd = ParmedCmd(self.parm, stdin=open(action.filename, 'r'),
stdout=self.stdout)
_cmd.prompt = ''
_cmd.interpreter = self.interpreter
_cmd.use_rawinput = 0
_cmd.cmdloop()
def addatomicnumber(root, amber_prmtop, messages):
""" Asks the user if they want to add ATOMIC_NUMBER to the prmtop """
response = askyesno('addAtomicNumber',
'Do you want to add the ATOMIC_NUMBER section to %s?' %
amber_prmtop.parm)
if response:
action = ParmedActions.addatomicnumber(amber_prmtop, ArgumentList(''))
action.execute()
messages.write('%s\n' % action)
def loadrestrt(root, amber_prmtop, messages):
""" Finds a file to load as a restart """
type_list = [('Inpcrd', '*.inpcrd'), ('Inpcrd', '*.crd'),
('Restart', '*.restrt'), ('Restart', '*.rst7'),
('All Files', '*')]
fname = file_chooser('Amber Coordinate File', type_list)
if fname:
action = ParmedActions.loadrestrt(amber_prmtop, ArgumentList(fname))
messages.write('%s\n' % action)
action.execute()
def printpointers(root, amber_prmtop, messages):
""" Prints all of the flags in the topology file """
window = Toplevel(root)
window.resizable(True, True)
window.title('POINTER list in %s' % amber_prmtop)
text = _guiwidgets.ExitingScrollText(window, None, spacing3=5, padx=5,
pady=5, width=80, height=20)
text.pack(fill=BOTH, expand=1)
action = ParmedActions.printpointers(amber_prmtop, ArgumentList(''))
text.write(action)
window.wait_window()
def netcharge(root, amber_prmtop, messages):
""" Calculates the net charge and shows its value """
mask = StringVar()
cmd_window = Toplevel(root)
mask_entry = _guiwidgets.MaskEntry(cmd_window, amber_prmtop,
'Mask from which to calculate charge', mask, cmd_window)
mask_entry.config(pady=10)
mask_entry.grid(row=0, column=0, sticky=N+E+S+W)
button = Button(cmd_window, text='OK / Quit', command=cmd_window.destroy)
button.grid(row=1, column=0, sticky=N+E+S+W)
cmd_window.wait_window()
if not mask.get(): return
action = ParmedActions.netcharge(amber_prmtop, ArgumentList(mask.get()))
chg = action.execute()
showinfo('Net Charge', 'The net charge of [%s] is %.4f' % (mask.get(), chg))
def checkvalidity(root, amber_prmtop, messages):
""" Basic validity checks """
# Create our Info window
window = Toplevel(root)
window.resizable(True, True)
window.title('Problems with %s' % amber_prmtop)
text = _guiwidgets.ExitingScrollText(window, None, spacing3=2, padx=5,
pady=5, width=81, height=30)
text.pack(fill=BOTH, expand=1)
# Set this text to catch the output of our action
ParmedActions.checkvalidity.output = text
# Initialize our action
action = ParmedActions.checkvalidity(amber_prmtop, ArgumentList(''))
messages.write('%s\n' % action)
action.execute()
text.write(action)
window.wait_window()
def changeradii(root, amber_prmtop, messages):
""" Allows users to change the GB Radius set """
title = 'Choose a Radius Set'
desc = ('Select a radius set for implicit solvent\n' +
'calculations. This has the same effect as\n' +
'"set default PBRadii <value>" in tleap')
radius_selection = StringVar()
namelist = ['bondi', 'mbondi', 'mbondi2', 'mbondi3', 'amber6']
cmd_window = _guiwidgets.RadioButtonWindow(
amber_prmtop, title, desc, radius_selection, namelist)
# Wait until the window is destroyed, then get the variable and pass it
# over to the class
cmd_window.wait_window()
sel = str(radius_selection.get())
if sel:
action = ParmedActions.changeradii(amber_prmtop, ArgumentList(sel))
messages.write('%s\n' % action)
action.execute()
def adddihedral(root, amber_prmtop, messages):
""" Adds a dihedral (improper, multiterm, or normal) to the prmtop """
# We need 4 masks, phi_k, periodicity, phase, scee/scnb, dihedral type
widget_list = [
('MaskEntry', 'First (end) atom in dihedral'),
('MaskEntry', 'Second (middle) atom in dihedral'),
('MaskEntry', 'Third (middle) atom in dihedral'),
('MaskEntry', 'Fourth (end) atom in dihedral'),
('Entry', 'Phi Force constant (kcal/mol)'),
('Entry', 'Periodicity'),
('Entry', 'Phase (Degrees)'),
('Entry', 'EEL scaling factor'),
('Entry', 'VDW scaling factor'),
('Spinbox', 'Dihedral type', 'normal', 'multiterm', 'improper')
]
# We need 10 variables
var_list = [StringVar() for i in range(10)]
description = ('Adds a dihedral in the topology file with the given Phi '
'Force constant in kcal/mol the\ngiven phase in Degrees '
'and the given periodicity. All masks must specify only \n'
'a single atom. The default Amber values for SCEE/SCNB are '
'1.2 and 2.0, respectively.\nSee the Amber manual for '
'details about normal, multiterm, and improper dihedrals')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('setDihedral', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
# If we did, pass them through
var_list = [v.get() for v in var_list]
# Fill scee/scnb in with default values
if var_list[7] is None: var_list[7] = '1.2'
if var_list[8] is None: var_list[8] = '2.0'
# The last argument is a keyword, so append that, then swap the last 2 args
var_list.insert(9, 'type')
try:
action = ParmedActions.adddihedral(amber_prmtop, ArgumentList(var_list))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def printljmatrix(root, amber_prmtop, messages):
""" Prints A/B matrix coefficients """
# We need 1 mask
widget_list = [('MaskEntry', 'Atoms To Find LJ Interactions')]
# We need 1 variable
var_list = [StringVar()]
description = ('Prints all A- and B-Coefficient elements between the atom ' +
'types specified in <mask> with every other atom type')
# Create the window, open it, and wait for it to close
cmd_window = _guiwidgets.ActionWindow('printLJMatrix', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# Bail out if we cancelled or something
var = var_list[0].get()
if not var: return
try:
action = ParmedActions.printljmatrix(amber_prmtop, ArgumentList(var))
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def addcoarsegrain(root, amber_prmtop, messages):
""" Adds coarse graining to topology file via Lula's algo """
# This implementation doesn't exist anywhere yet, so disable it
showerror('Warning', 'This functionality is not implemented in Amber yet!')
return
# We need a file
fname = file_chooser('Coarse Grain Parameter',
[('Coarse Grain Parameters', '*.cgparm'),
('All Files', '*')])
if not fname: return
try:
action = ParmedActions.addcoarsegrain(amber_prmtop, ArgumentList(fname))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def combinemolecules(root, amber_prmtop, messages):
""" Combines 2 molecules into a single molecule """
# We need a molecule #
widget_list = [('Entry', 'Molecule Number')]
var_list = [StringVar()]
description = 'Combine the given molecule number with the next molecule'
cmd_window = _guiwidgets.ActionWindow('combineMolecules', amber_prmtop,
widget_list, var_list, description)
cmd_window.wait_window()
# See if we got any variables back
var = var_list[0].get()
if not var: return
# addljtype expects any _non_specified variables to be None
try:
action = ParmedActions.combinemolecules(amber_prmtop, ArgumentList(var))
messages.write('%s\n' % action)
action.execute()
except Exception, err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return